NatLabRockies · malihass · Oct 20, 2025 · Oct 17, 2025 · Oct 17, 2025 · Oct 17, 2025
diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
@@ -25,19 +25,22 @@ jobs:
           python-version: '3.10'
           cache: 'pip'
 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          micromamba install --yes -n test-env -c conda-forge paraview
           python -m pip install --upgrade pip
-          pip install -e .
+          pip install -e . 
           pip install sphinx sphinx_rtd_theme sphinx-autodoc-typehints
 
       - name: Build documentation

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -66,19 +66,22 @@ jobs:
         with:
           python-version: ${{matrix.python-version}}
 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
-          pip install .
+          pip install . 
           pip install pytest
 
       - name: Test
@@ -102,17 +105,20 @@ jobs:
         with:
           python-version: ${{matrix.python-version}}
 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
           pip install nrel-bird
           pip install pytest
@@ -141,17 +147,20 @@ jobs:
         with:
           openfoam-version: 9
 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
           pip install .
 

diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
@@ -27,17 +27,20 @@ jobs:
           python-version: '3.13'
           cache: 'pip'
 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
           pip install pytest
           pip install pytest-cov

diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml
@@ -26,18 +26,21 @@ jobs:
         with:
           python-version: '3.10'
           cache: 'pip'
- 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
           pip install -e .
           pip install sphinx sphinx_rtd_theme sphinx-autodoc-typehints

diff --git a/applications/write_stl_patch.py b/applications/write_stl_patch.py
@@ -32,8 +32,8 @@
 
     if args.verbose:
         # plot
-        from bird.utilities.stl_plotting import plotSTL, plt, pretty_labels
+        from bird.utilities.stl_plotting import plot_stl, plt, pretty_labels
 
-        axes = plotSTL("inlets.stl")
+        axes = plot_stl("inlets.stl")
         pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)
         plt.show()
diff --git a/bird/calibration/param_nn.py b/bird/calibration/param_nn.py
@@ -1,6 +1,7 @@
 import argparse
 import os
 import time
+from pathlib import Path
 
 import joblib
 import numpy as np
@@ -306,8 +307,8 @@ def load(self, weight_file):
         self.model.load_weights(weight_file)
 
     def prepareLog(self):
-        os.makedirs(self.model_folder, exist_ok=True)
-        os.makedirs(self.log_loss_folder, exist_ok=True)
+        Path(self.model_folder).mkdir(parents=True, exist_ok=True)
+        Path(self.log_loss_folder).mkdir(parents=True, exist_ok=True)
         try:
             os.remove(os.path.join(self.log_loss_folder, "log.csv"))
         except FileNotFoundError as err:

diff --git a/bird/logging_config.py b/bird/logging_config.py
@@ -6,9 +6,7 @@ class ConditionalFormatter(logging.Formatter):
     def format(self, record):
         """Change how to log if it is an INFO or a WARNING/ERROR"""
         if record.levelno >= logging.WARNING:
-            self._style._fmt = (
-                "%(asctime)s [%(levelname)s] %(name)s: %(message)s"
-            )
+            self._style._fmt = "%(asctime)s [%(levelname)s] bird: %(message)s"
         else:
             self._style._fmt = "%(asctime)s [%(levelname)s] bird: %(message)s"
         return super().format(record)

diff --git a/bird/meshing/_mesh_tools.py b/bird/meshing/_mesh_tools.py
@@ -1,6 +1,7 @@
 import numpy as np
 
 from bird import logger
+from bird.utilities.mathtools import bissection
 
 
 def make_walls_from_topo(topo_dict: dict) -> dict:
@@ -70,8 +71,8 @@ def make_bound_from_topo(topo_dict):
     }
 
 
-def stretch_fun(G, N1):
-    result = (1.0 - G) / (G * (1 - np.power(G, 1.0 / N1)))
+def stretch_fun(G, N):
+    result = (1.0 - G) / (G * (1 - np.power(G, 1.0 / N)))
     return result
 
 
@@ -80,29 +81,6 @@ def stretch_fun(G, N1):
 #    return result
 
 
-def bissection(val, stretch_fun, N1):
-    Gmin = 0.00001
-    Gmax = 1000000
-    resultmin = stretch_fun(Gmin, N1) - val
-    resultmax = stretch_fun(Gmax, N1) - val
-    if resultmin * resultmax > 0:
-        error_msg = "Initial bounds of grading do not encompass the solution"
-        logger.error(error_msg)
-        raise ValueError(error_msg)
-
-    for i in range(1000):
-        Gmid = 0.5 * (Gmax + Gmin)
-        resultmid = stretch_fun(Gmid, N1) - val
-        if resultmid * resultmax < 0:
-            Gmin = Gmid
-            resultmin = resultmid
-        else:
-            Gmax = Gmid
-            resultmax = resultmid
-
-    return Gmid
-
-
 def is_wall(l_wall: list[int], r_wall: list[int], ir: int, il: int) -> int:
     """
     Is the present block a wall (not meshed)
@@ -223,19 +201,17 @@ def verticalCoarsening(
                 raise ValueError(error_msg)
 
             if ratio_dir[ind] == "+":
-                gradVert[ind] = 1.0 / bissection(
-                    length / deltaE, stretch_fun, NVert[ind]
-                )
+                nl_func = lambda x: stretch_fun(x, NVert[ind])
+                gradVert[ind] = 1.0 / bissection(length / deltaE, nl_func)
                 iterate = False
                 origNVert = NVert[ind]
                 while gradVert[ind] < 1 and NVert[ind] > 1:
                     iterate = True
                     NVert[ind] = max(
                         int(round(min(0.99 * NVert[ind], NVert[ind] - 1))), 1
                     )
-                    gradVert[ind] = 1.0 / bissection(
-                        length / deltaE, stretch_fun, NVert[ind]
-                    )
+                    nl_func = lambda x: stretch_fun(x, NVert[ind])
+                    gradVert[ind] = 1.0 / bissection(length / deltaE, nl_func)
                 if iterate:
                     logger.warning(
                         f"reduced NVert[{ind}] from {origNVert} to {NVert[ind]}"
@@ -245,9 +221,8 @@ def verticalCoarsening(
 
             elif ratio_dir[ind] == "-":
                 deltaE = block_cell_minus_length[ind - 1]
-                gradVert[ind] = bissection(
-                    length / deltaE, stretch_fun, NVert[ind]
-                )
+                nl_func = lambda x: stretch_fun(x, NVert[ind])
+                gradVert[ind] = bissection(length / deltaE, nl_func)
 
                 iterate = False
                 origNVert = NVert[ind]
@@ -256,9 +231,8 @@ def verticalCoarsening(
                     NVert[ind] = max(
                         int(round(min(0.99 * NVert[ind], NVert[ind] - 1))), 1
                     )
-                    gradVert[ind] = bissection(
-                        length / deltaE, stretch_fun, NVert[ind]
-                    )
+                    nl_func = lambda x: stretch_fun(x, NVert[ind])
+                    gradVert[ind] = bissection(length / deltaE, nl_func)
                 if iterate:
                     logger.warning(
                         f"reduced NVert[{ind}] from {origNVert} to {NVert[ind]}"
@@ -337,19 +311,17 @@ def radialCoarsening(
                 raise ValueError(error_msg)
 
             if ratio_dir[ind] == "+":
-                gradR[ind] = 1.0 / bissection(
-                    length / deltaE, stretch_fun, NR[ind]
-                )
+                nl_func = lambda x: stretch_fun(x, NR[ind])
+                gradR[ind] = 1.0 / bissection(length / deltaE, nl_func)
                 iterate = False
                 origNR = NR[ind]
                 while gradR[ind] < 1 and NR[ind] > 1:
                     iterate = True
                     NR[ind] = max(
                         int(round(min(0.99 * NR[ind], NR[ind] - 1))), 1
                     )
-                    gradR[ind] = 1.0 / bissection(
-                        length / deltaE, stretch_fun, NR[ind]
-                    )
+                    nl_func = lambda x: stretch_fun(x, NR[ind])
+                    gradR[ind] = 1.0 / bissection(length / deltaE, nl_func)
                 if iterate:
                     logger.warning(
                         f"reduced NR[{ind}] from {origNR} to {NR[ind]}"
@@ -359,15 +331,15 @@ def radialCoarsening(
 
             elif ratio_dir[ind] == "-":
                 deltaE = block_cell_minus_length[ind - 1]
-                gradR[ind] = bissection(length / deltaE, stretch_fun, NR[ind])
+                nl_func = lambda x: stretch_fun(x, NR[ind])
+                gradR[ind] = bissection(length / deltaE, nl_func)
                 iterate = False
                 origNR = NR[ind]
                 while gradR[ind] > 1 and NR[ind] > 1:
                     iterate = True
                     NR[ind] = max(int(round(min(0.99 * NR[ind], -1))), 1)
-                    gradR[ind] = bissection(
-                        length / deltaE, stretch_fun, NR[ind]
-                    )
+                    nl_func = lambda x: stretch_fun(x, NR[ind])
+                    gradR[ind] = bissection(length / deltaE, nl_func)
                 if iterate:
                     logger.warning(
                         f"reduced NR[{ind}] from {origNR} to {NR[ind]}"

diff --git a/bird/meshing/block_cyl_mesh.py b/bird/meshing/block_cyl_mesh.py
@@ -550,12 +550,3 @@ def writeBlockMeshDict(out_folder, geom_dict, mesh_dict):
 
     fw.close()
 
-
-def main(input_file, topo_file, output_folder):
-    geom_dict = assemble_geom(input_file, topo_file)
-    mesh_dict = assemble_mesh(input_file, geom_dict)
-    writeBlockMeshDict(output_folder, geom_dict, mesh_dict)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/bird/postprocess/early_pred.py b/bird/postprocess/early_pred.py
@@ -102,7 +102,9 @@ def multi_data_load(data_root, tmax=600, data_files=None, color_files=None):
         A = np.loadtxt(filename)
         data_dict[datf] = {}
         data_dict[datf]["t"] = A[:, 0]
-        data_dict[datf]["y"] = A[:, 5] / (A[:, 4] * 16 / 44 + A[:, 5])
+        data_dict[datf]["y"] = A[:, 5] / np.clip(
+            (A[:, 4] * 16 / 44 + A[:, 5]), a_min=1e-12, a_max=None
+        )
         # chop data before increase and right after t=10s
         increase_ind_arr = np.argwhere(np.diff(data_dict[datf]["y"]) > 0)
         increase_ind = increase_ind_arr[
@@ -264,13 +266,3 @@ def bayes_fit(data_dict, num_warmup=1000, num_samples=500):
 
     return data_dict
 
-
-if __name__ == "__main__":
-    from bird import BIRD_EARLY_PRED_DATA_DIR
-
-    data_dict, color_files = multi_data_load(BIRD_EARLY_PRED_DATA_DIR)
-    data_dict = fit_and_ext(data_dict)
-    plotAllEarly(data_dict, color_files=color_files, chop=True, extrap=True)
-    bayes_fit(data_dict)
-    plotAllEarly_uq(data_dict, color_files=color_files)
-    plt.show()
diff --git a/bird/postprocess/kla_utils.py b/bird/postprocess/kla_utils.py
@@ -371,7 +371,3 @@ def print_res_dict(res_dict: dict) -> None:
     logger.info(f"\tkla = {kla_nb*3600:.4g} +/- {kla_err_nb*3600:.4g} [h-1]")
     logger.info(f"\tcstar = {cs_nb:.4g} +/- {cs_err_nb:.4g} [mol/m3]")
 
-
-if __name__ == "__main__":
-    res_dict = compute_kla("data_kla/volume_avg.dat", time_ind=0, conc_ind=1)
-    print_res_dict(res_dict)